:orphan: .. only available via index, not via toctree .. title:: Package Recipe 'bioconductor-phyloprofile' .. highlight: bash bioconductor-phyloprofile ========================= .. conda:recipe:: bioconductor-phyloprofile :replaces_section_title: :noindex: PhyloProfile :homepage: https://bioconductor.org/packages/3.18/bioc/html/PhyloProfile.html :license: MIT + file LICENSE :recipe: /`bioconductor-phyloprofile `_/`meta.yaml `_ PhyloProfile is a tool for exploring complex phylogenetic profiles. Phylogenetic profiles\, presence\/absence patterns of genes over a set of species\, are commonly used to trace the functional and evolutionary history of genes across species and time. With PhyloProfile we can enrich regular phylogenetic profiles with further data like sequence\/structure similarity\, to make phylogenetic profiling more meaningful. Besides the interactive visualisation powered by R\-Shiny\, the package offers a set of further analysis features to gain insights like the gene age estimation or core gene identification. .. conda:package:: bioconductor-phyloprofile |downloads_bioconductor-phyloprofile| |docker_bioconductor-phyloprofile| :versions: .. raw:: html
1.16.0-01.14.5-01.12.0-01.8.0-01.6.1-01.4.9-01.4.0-01.2.8-11.2.6-0 ``1.16.0-0``,  ``1.14.5-0``,  ``1.12.0-0``,  ``1.8.0-0``,  ``1.6.1-0``,  ``1.4.9-0``,  ``1.4.0-0``,  ``1.2.8-1``,  ``1.2.6-0``,  ``1.2.5-0``,  ``1.2.2-0``,  ``1.0.1-0`` .. raw:: html
:depends bioconductor-biocstyle: ``>=2.30.0,<2.31.0`` :depends bioconductor-biodist: ``>=1.74.0,<1.75.0`` :depends bioconductor-biostrings: ``>=2.70.0,<2.71.0`` :depends bioconductor-experimenthub: ``>=2.10.0,<2.11.0`` :depends bioconductor-omadb: ``>=2.18.0,<2.19.0`` :depends r-ape: :depends r-base: ``>=4.3,<4.4.0a0`` :depends r-colourpicker: :depends r-data.table: :depends r-dt: :depends r-energy: :depends r-ggplot2: :depends r-gridextra: :depends r-pbapply: :depends r-plyr: :depends r-rcolorbrewer: :depends r-rcurl: :depends r-shiny: :depends r-shinybs: :depends r-shinycssloaders: :depends r-shinyfiles: :depends r-shinyjs: :depends r-stringr: :depends r-xml2: :depends r-yaml: :depends r-zoo: :requirements: .. rubric:: Installation You need a conda-compatible package manager (currently either `micromamba `_, `mamba `_, or `conda `_) and the Bioconda channel already activated (see :ref:`set-up-channels`). While any of above package managers is fine, it is currently recommended to use either micromamba or mamba (see `here `_ for installation instructions). We will show all commands using mamba below, but the arguments are the same for the two others. Given that you already have a conda environment in which you want to have this package, install with:: mamba install bioconductor-phyloprofile and update with:: mamba update bioconductor-phyloprofile To create a new environment, run:: mamba create --name myenvname bioconductor-phyloprofile with ``myenvname`` being a reasonable name for the environment (see e.g. the `mamba docs `_ for details and further options). Alternatively, use the docker container:: docker pull quay.io/biocontainers/bioconductor-phyloprofile: (see `bioconductor-phyloprofile/tags`_ for valid values for ````) .. |downloads_bioconductor-phyloprofile| image:: https://img.shields.io/conda/dn/bioconda/bioconductor-phyloprofile.svg?style=flat :target: https://anaconda.org/bioconda/bioconductor-phyloprofile :alt: (downloads) .. |docker_bioconductor-phyloprofile| image:: https://quay.io/repository/biocontainers/bioconductor-phyloprofile/status :target: https://quay.io/repository/biocontainers/bioconductor-phyloprofile .. _`bioconductor-phyloprofile/tags`: https://quay.io/repository/biocontainers/bioconductor-phyloprofile?tab=tags .. raw:: html Download stats ----------------- .. raw:: html :file: ../../templates/package_dashboard.html Link to this page ----------------- Render an |install-with-bioconda| badge with the following MarkDown:: [![install with bioconda](https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat)](http://bioconda.github.io/recipes/bioconductor-phyloprofile/README.html) .. |install-with-bioconda| image:: https://img.shields.io/badge/install%20with-bioconda-brightgreen.svg?style=flat :target: http://bioconda.github.io/recipes/bioconductor-phyloprofile/README.html